Systems and methods for sample preparation, data generation, and protein corona analysis
Inventors
Manning, William • Kim, Young • Kwan-Leong, Brandon • Liou, Hope • Zhao, Xiaoyan • Hornburg, Daniel • Goldberg, Martin
Assignees
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Publication Number
US-11906526-B2
Publication Date
2024-02-20
Expiration Date
Abstract
Systems and methods for automated sample preparation and processing of protein corona are described herein, as well as its application in the discovery of advanced diagnostic tools as well as therapeutic agents.
Core Innovation
The invention relates to an automated system that performs sample preparation using a multichannel fluid transfer unit and a magnetic sensor array to form protein coronas on magnetic particles. A biological sample is incubated with a diluent and a plurality of magnetic particles in partitions of the magnetic sensor array so that proteins from the biological sample interact with the magnetic particles. The magnetic support immobilizes the plurality of magnetic particles when the magnetic sensor array is transferred to the magnetic support.
After incubation, a supernatant is removed from the partitions to isolate the proteins interacting with the magnetic particles, and the interacting proteins are washed. A population of peptides is then prepared for mass spectrometry by incubating a digestion solution with the washed proteins and at least one of the plurality of magnetic particles. The system uses agitation and/or mixing during incubation in the specified temperature range for a specified duration.
The magnetic particles are configured to bind at least 300 different proteins from the biological sample, enabling a broad protein interaction profile on the sensor elements. The disclosed examples describe forming patient-specific biomolecule fingerprints from corona protein relative abundances across multiple particle types, followed by computational comparison to disease-state reference fingerprints. The described disease context includes cancer detection and staging across pre-, early, intermediate, and late disease stages, including NSCLC versus healthy controls.
Claims Coverage
The partial content provides one independent claim covering an automated sample-preparation system. The main inventive features are distributed across the magnetic sensor array configuration and the controlled steps of incubating, isolating, washing, and preparing peptides for mass spectrometry, with supportive constraints on particle binding capacity and particle characteristics in dependent claims.
Automated system with multichannel fluid transfer and magnetic sensor array partitions
An automated system comprising a multichannel fluid transfer instrument, and a sensor array with a magnetic support and a magnetic sensor array having a plurality of partitions, where at least one partition comprises a biological sample, a diluent with buffer, and a plurality of magnetic particles.
Magnetic particles immobilized on transfer to magnetic support
The plurality of magnetic particles comprise silica and a carboxyl functionalized surface, at least one magnetic particle configured to bind at least 300 different proteins from the biological sample, and the magnetic support configured to immobilize the plurality of magnetic particles when the magnetic sensor array is transferred to the magnetic support.
Control unit performing incubation to form protein interactions with agitation and/or mixing
A control unit with one or more processors programmed to perform incubating the biological sample and diluent with the plurality of magnetic particles in the partitions such that proteins from the biological sample interact with the magnetic particles, using agitation and/or mixing at 4°C to 40°C for at least 20 minutes.
Isolation and washing of corona-associated proteins followed by peptide preparation for mass spectrometry
Removing a supernatant from the partitions to isolate the proteins interacting with the magnetic particles; washing the interacting proteins to obtain washed proteins; and preparing a population of peptides for mass spectrometry by incubating a digestion solution with the washed proteins and at least one of the magnetic particles.
Claim coverage centers on automating protein corona-based capture in a magnetic sensor array using multichannel transfer, then executing incubate, supernatant removal, washing, and peptide preparation steps under specified incubation conditions for subsequent mass spectrometry.
Stated Advantages
Enables high-coverage proteomic measurements.
High accuracy/certainty for biological state classification, including disease state classification such as early-stage cancer.
Forms patient-specific biomolecule fingerprints from corona protein relative abundances across multiple particle types.
Enables computational comparison to disease-state reference fingerprints.
Supports cancer detection and staging across pre-, early, intermediate, and late disease stages, including NSCLC versus healthy controls.
Documented Applications
Disease state classification, including early-stage cancer, using proteomics measurements derived from biomolecule corona signatures and a biomolecule fingerprint based on mass spectrometry signals [procedural detail omitted for safety].
Cancer detection and staging.
NSCLC versus healthy controls.
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